Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1978 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0500533542 sf0500533542 5 533542 2.45E-07 2.46E-07
vg0917690607 sf0917689606 9 17690607 2.58E-07 2.58E-07
vg0627335333 sf0627334336 6 27335333 4.17E-07 4.18E-07
vg0321136492 sf0321135002 3 21136492 4.32E-07 4.32E-07
vg0202528514 sf0202528512 2 2528514 1.28E-06 1.29E-06
vg1123899687 sf1123433557 11 23899687 1.40E-06 1.41E-06
vg1018801376 sf1018729933 10 18801376 1.62E-06 1.62E-06
vg0607146466 sf0607145467 6 7146466 2.24E-06 2.25E-06